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NASA NTRS2001

The New Cloud Absorption Radiometer (CAR) Software: One Model for NASA Remote Sensing Virtual Instruments

The Cloud Absorption Radiometer (CAR) instrument has been the most frequently used airborne instrument built in-house at NASA Goddard Space Flight Center, having flown scientific research missions on-board various aircraft to many locations in the United States, Azores, Brazil, and Kuwait since 1983. The CAR instrument is capable of measuring scattered light by clouds in fourteen spectral bands in UV, visible and near-infrared region. This document describes the control, data acquisition, display, and file storage software for the new version of CAR. This software completely replaces the prior CAR Data System and Control Panel with a compact and robust virtual instrument computer interface. Additionally, the instrument is now usable for the first time for taking data in an off-aircraft mode. The new instrument is controlled via a LabVIEW v5. 1.1-developed software interface that utilizes, (1) serial port writes to write commands to the controller module of the instrument, and (2) serial port reads to acquire data from the controller module of the instrument. Step-by-step operational procedures are provided in this document. A suite of other software programs has been developed to complement the actual CAR virtual instrument. These programs include: (1) a simulator mode that allows pretesting of new features that might be added in the future, as well as demonstrations to CAR customers, and development at times when the instrument/hardware is off-location, and (2) a post-experiment data viewer that can be used to view all segments of individual data cycles and to locate positions where 'start' and stop' byte sequences were incorrectly formulated by the instrument controller. The CAR software described here is expected to be the basis for CAR operation for many missions and many years to come.

Roth, Don J.↗

NASA NTRS1996

Macular Preprocessing of Linear Acceleratory Stimuli: Implications for the Clinic

Three-dimensional reconstructions of innervation patterns in rat maculae were carried out using serial section images sent to a Silicon Graphics workstation from a transmission electron microscope. Contours were extracted from mosaicked sections, then registered and visualized using Biocomputation Center software. Purposes were to determine innervation patterns of type II cells and areas encompassed by vestibular afferent receptive fields. Terminals on type II cells typically are elongated and compartmentalized into parts varying in vesicular content; reciprocal and serial synapses are common. The terminals originate as processes of nearby calyces or from nerve fibers passing to calyces outside the immediate vicinity. Thus, receptive fields of the afferents overlap in unique ways. Multiple processes are frequent; from 4 to 6 afferents supply 12-16 terminals on a type II cell. Processes commonly communicate with two type II cells. The morphology indicates that extensive preprocessing of linear acceleratory stimuli occurs peripherally, as is true also of visual and olfactory systems. Clinically, this means that loss of individual nerve fibers may not be noticed behaviorally, due to redundancy (receptive field overlap). However, peripheral processing implies the presence of neuroactive agents whose loss can acutely or chronically alter normal peripheral function and cause balance disorders. (Platform presentation preferred - Theme 11)

Ross, M. D.↗

NASA NTRS1996

3-D Imaging In Virtual Environment: A Scientific Clinical and Teaching Tool

The advent of powerful graphics workstations and computers has led to the advancement of scientific knowledge through three-dimensional (3-D) reconstruction and imaging of biological cells and tissues. The Biocomputation Center at NASA Ames Research Center pioneered the effort to produce an entirely computerized method for reconstruction of objects from serial sections studied in a transmission electron microscope (TEM). The software developed, ROSS (Reconstruction of Serial Sections), is now being distributed to users across the United States through Space Act Agreements. The software is in widely disparate fields such as geology, botany, biology and medicine. In the Biocomputation Center, ROSS serves as the basis for development of virtual environment technologies for scientific and medical use. This report will describe the Virtual Surgery Workstation Project that is ongoing with clinicians at Stanford University Medical Center, and the role of the Visible Human data in the project.

Ross, Muriel D.↗

NASA NTRS2002

Relative Debugging of Automatically Parallelized Programs

We describe a system that simplifies the process of debugging programs produced by computer-aided parallelization tools. The system uses relative debugging techniques to compare serial and parallel executions in order to show where the computations begin to differ. If the original serial code is correct, errors due to parallelization will be isolated by the comparison. One of the primary goals of the system is to minimize the effort required of the user. To that end, the debugging system uses information produced by the parallelization tool to drive the comparison process. In particular, the debugging system relies on the parallelization tool to provide information about where variables may have been modified and how arrays are distributed across multiple processes. User effort is also reduced through the use of dynamic instrumentation. This allows us to modify, the program execution with out changing the way the user builds the executable. The use of dynamic instrumentation also permits us to compare the executions in a fine-grained fashion and only involve the debugger when a difference has been detected. This reduces the overhead of executing instrumentation.

Jost, Gabriele↗

NASA NTRS1998

Parallelization of ARC3D with Computer-Aided Tools

A series of efforts have been devoted to investigating methods of porting and parallelizing applications quickly and efficiently for new architectures, such as the SCSI Origin 2000 and Cray T3E. This report presents the parallelization of a CFD application, ARC3D, using the computer-aided tools, Cesspools. Steps of parallelizing this code and requirements of achieving better performance are discussed. The generated parallel version has achieved reasonably well performance, for example, having a speedup of 30 for 36 Cray T3E processors. However, this performance could not be obtained without modification of the original serial code. It is suggested that in many cases improving serial code and performing necessary code transformations are important parts for the automated parallelization process although user intervention in many of these parts are still necessary. Nevertheless, development and improvement of useful software tools, such as Cesspools, can help trim down many tedious parallelization details and improve the processing efficiency.

Jin, Haoqiang↗

NASA NTRS1998

Charon Message-Passing Toolkit for Scientific Computations

The Charon toolkit for piecemeal development of high-efficiency parallel programs for scientific computing is described. The portable toolkit, callable from C and Fortran, provides flexible domain decompositions and high-level distributed constructs for easy translation of serial legacy code or design to distributed environments. Gradual tuning can subsequently be applied to obtain high performance, possibly by using explicit message passing. Charon also features general structured communications that support stencil-based computations with complex recurrences. Through the separation of partitioning and distribution, the toolkit can also be used for blocking of uni-processor code, and for debugging of parallel algorithms on serial machines. An elaborate review of recent parallelization aids is presented to highlight the need for a toolkit like Charon. Some performance results of parallelizing the NAS Parallel Benchmark SP program using Charon are given, showing good scalability.

VanderWijngaart, Rob F.↗

NASA NTRS1997

Three-Dimensional Analysis of Nuclear Size, Shape and Displacement in Clover Root Cap Statocytes from Space and a Clinostat

Under normal (l-g) conditions the statocytes of root caps have a characteristic polarity with the nucleus in tight association with the proximal cell wall; but, in altered gravity environments including microgravity (mu-g) and the clinostat (c-g) movement of the nucleus away from the proximal cell wall is not uncommon. To further understand the cause of gravity-dependent nuclear displacement in statocytes, three-dimensional cell reconstruction techniques were used to precisely measure the volumes, shapes, and positions of nuclei in white clover (Trifolium repens) flown in space and rotated on a clinostat. Seeds were germinated and grown for 72 hours aboard the Space Shuttle (STS-63) in the Fluid Processing Apparatus (BioServe Space Technologies, Univ. of Colorado, Boulder). Clinorotation experiments were performed on a two-axis clinostat (BioServe). Computer reconstruction of selected groups of statocytes were made from serial sections (0.5 microns thick) using the ROSS (Reconstruction Of Serial Sections) software package (Biocomputation Center, NASA Ames Research Center). Nuclei were significantly displaced from the tops of cells in mu-g (4.2 +/- 1.0 microns) and c-g (4.9 +/- 1.4 microns) when compared to l-g controls (3.4 +/- 0.8 gm); but, nuclear volume (113 +/- 36 cu microns, 127 +/- 32 cu microns and 125 +/- 28 cu microns for l-g, mu-g and c-g respectively) and the ratio of nuclear volume to cell volume (4.310.7%, 4.211.0% and 4.911.4% respectively) were not significantly dependent on gravity treatment (ANOVA; alpha = 0.05). Three-dimensional analysis of nuclear shape and proximity to the cell wall, however, showed that nuclei from l-g controls appeared ellipsoidal while those from space and the clinostat were more spherically shaped. This change in nuclear shape may be responsible for its displacement under altered gravity conditions. Since the cytoskeleton is known to affect nuclear polarity in root cap statocytes, those same cytoskeletal elements could also control nuclear shape. This alteration in nuclear shape and position in mu-g and c-g when compared to l-g may lead to functional differences in the gravity signaling systems of plants subjected to altered gravity environments.

Smith, J.D.↗

NASA NTRS1998

Charon Message-Passing Toolkit for Scientific Computations

VanderWijngarrt, Rob F.↗

NASA NTRS1998

Legacy Code Modernization

Over the past decade, high performance computing has evolved rapidly; systems based on commodity microprocessors have been introduced in quick succession from at least seven vendors/families. Porting codes to every new architecture is a difficult problem; in particular, here at NASA, there are many large CFD applications that are very costly to port to new machines by hand. The LCM ("Legacy Code Modernization") Project is the development of an integrated parallelization environment (IPE) which performs the automated mapping of legacy CFD (Fortran) applications to state-of-the-art high performance computers. While most projects to port codes focus on the parallelization of the code, we consider porting to be an iterative process consisting of several steps: 1) code cleanup, 2) serial optimization,3) parallelization, 4) performance monitoring and visualization, 5) intelligent tools for automated tuning using performance prediction and 6) machine specific optimization. The approach for building this parallelization environment is to build the components for each of the steps simultaneously and then integrate them together. The demonstration will exhibit our latest research in building this environment: 1. Parallelizing tools and compiler evaluation. 2. Code cleanup and serial optimization using automated scripts 3. Development of a code generator for performance prediction 4. Automated partitioning 5. Automated insertion of directives. These demonstrations will exhibit the effectiveness of an automated approach for all the steps involved with porting and tuning a legacy code application for a new architecture.

Hribar, Michelle R.↗

NASA NTRS2002

Backtracking and Re-execution in the Automatic Debugging of Parallelized Programs

In this work we describe a new approach using relative debugging to find differences in computation between a serial program and a parallel version of th it program. We use a combination of re-execution and backtracking in order to find the first difference in computation that may ultimately lead to an incorrect value that the user has indicated. In our prototype implementation we use static analysis information from a parallelization tool in order to perform the backtracking as well as the mapping required between serial and parallel computations.

Matthews, Gregory↗

NASA NTRS2001

Support for Debugging Automatically Parallelized Programs

We describe a system that simplifies the process of debugging programs produced by computer-aided parallelization tools. The system uses relative debugging techniques to compare serial and parallel executions in order to show where the computations begin to differ. If the original serial code is correct, errors due to parallelization will be isolated by the comparison. One of the primary goals of the system is to minimize the effort required of the user. To that end, the debugging system uses information produced by the parallelization tool to drive the comparison process. In particular the debugging system relies on the parallelization tool to provide information about where variables may have been modified and how arrays are distributed across multiple processes. User effort is also reduced through the use of dynamic instrumentation. This allows us to modify the program execution without changing the way the user builds the executable. The use of dynamic instrumentation also permits us to compare the executions in a fine-grained fashion and only involve the debugger when a difference has been detected. This reduces the overhead of executing instrumentation.

Jost, Gabriele↗

NASA NTRS2002

Wireless Temperature-Monitoring System

A relatively inexpensive instrumentation system that includes units that are connected to thermocouples and that are parts of a radio-communication network has been developed to enable monitoring of temperatures at multiple locations. Because there is no need to string wires or cables for communication, the system is well suited for monitoring temperatures at remote locations and for applications in which frequent changes of monitored or monitoring locations are needed. The system can also be adapted to monitoring of slowly varying physical quantities, other than temperature, that can be transduced by solid-state electronic sensors. electronic sensors. The system comprises any number of transmitting units and a single receiving unit. Each transmitting unit includes connections for as many as four external thermocouples, a signal-conditioning module, a control module, and a radio-communication module. The signal-conditioning module acts as an interface between the thermocouples and the rest of the transmitting unit and includes a built-in solid ambient temperature sensor that is in addition to the external thermocouples. The control module is a system-on-chip embedded processor that includes analog-to-digital converters, serial and parallel data ports, and an interface for local connection to an analog meter that is used during installation to verify correct operation. The radio-communication module contains a commercial spread-spectrum transceiver that operates in the 900-MHz industrial, scientific, and medical (ISM) frequency band. This transceiver transmits data to the receiving unit at a rate of 19,200 baud. The receiving unit includes a transceiver like that of a transmitting unit, plus a control module that contains a system-on-chip processor that includes serial data port for output to a computer that runs monitoring and/or control software, a parallel data port for output to a printer, and a seven-segment light-emitting-diode display. Each transmitting unit is battery-powered and can operate for at least seven days continuously while reporting temperatures every half hour. The receiving unit is powered by a wall-mounted transformer source. The receiving unit responds to each transmitting unit and reports the readings of each of the four thermocouples and of the ambient-temperature sensor of the transmitting unit. The end-to-end accuracy of the system is plus or minus 0.2 C over the temperature range from 0 to 100 C. The radio-communication range between the receiving and transmitting units is approximately equal to 0.5 mile (approximately equal to 0.8 km).

Solano, Wanda↗

NASA NTRS2003

Morphology of the Vestibular Utricule in Toadfish, Opsanus Tau

The uticle is an otolith organ in the vertebrate inner ear that provides gravitoinertial acceleration information into the vestibular reflex pathways. The aim of the present study was to provide an anatomical description of this structure in the adult oyster toadfish, and establish a morphological basis for interpretation of subsequent functional studies. Light, scanning electron and transmission electron microscopy were applied to visualize the sensory epithelium and its neural innervation. Electrophysiological techniques were used to identify utricular afferents by their response to translation stimuli. Similar to nerve afferents supplying the semicircular canals and lagena, utricular afferents commonly exhibit a short-latency increase of firing rate in response to electrical activation of the central efferent pathway. Afferents were labeled with biocytin either intraaxonally or with extracellular bulk deposits. Light microscope images of serial thick sections were used to make three-dimensional reconstructions of individual labeled afferents to identify the dendritic morphology with respect to epithelial location. Scanning electron microscopy was used to visualize the surface of the otolith mass facing the otolith membrane, and the hair cell polarization patterns of strioler and extrastriolar regions. Transmission electron micrographs of serial thin sections were compiled to create a three-dimensional reconstruction of the labeled afferent over a segment of its dendritic field and to examine the hair cell-afferent synaptic contacts.

Bass, L.↗

NASA NTRS2004

Adding HDLC Framing to CCSDS Recommendations

Current Space IP missions use High-Level Data Link Control (HDLC) framing to provide standard serial link interfaces over a space link. HDLC is the standard framing technique used by all routers over clock and data serial lines and is also the basic framing used in all Frame Relay services which are widely deployed in national and international communication networks. In late 2003 a presentation was made to CCSDS committees to initiate discussion on including HDLC in the CCSDS recommendations for space systems. This presentation will summarize the differences between variable length HDLC frames and fixed length CCSDS frames. It will also discuss where and how HDLC framing would fit into the overall CCSDS structures.

Hogie, Keith↗

NASA NTRS2003

An evaluation of the use of new Doppler methods for detecting longitudinal function abnormalities in a pacing-induced heart failure model

BACKGROUND: Doppler tissue echocardiography and color M-mode Doppler flow propagation velocity have proven useful in evaluating cross-sections of patients with left ventricular (LV) dysfunction, but experience with serial changes is limited. Purpose and methods: We tested their use by evaluating the temporal changes of LV function in a pacing-induced congestive heart failure model. Rapid ventricular pacing was initiated and maintained in 20 dogs for 4 weeks. Echocardiography was performed at baseline and weekly during brief pacing cessation. RESULTS: With rapid pacing, LV volume significantly increased and ejection fraction (57%-28%), stroke volume (37-18 mL), and mitral annulus systolic velocity (16.1-6.6 cm/s) by Doppler tissue echocardiography significantly decreased, with ejection fraction and mitral annulus systolic velocity closely correlated (r = 0.706, P <.0001). In contrast to the mitral inflow velocities, mitral annulus early diastolic velocity decreased steadily (12.3-7.3 cm/s) resulting in a dramatic decrease in mitral annulus early/late (1.22-0.57) diastolic velocity with no tendency toward pseudonormalization. The color M-mode Doppler flow propagation velocity also showed significant steady decrease (57-24 cm/s) throughout the pacing period. Multiple regression analysis chose mitral annulus systolic velocity (r = 0.895, P <.0001) and propagation velocity (r = 0.782, P <.0001) for the most important factor predicting LV systolic and diastolic function, respectively. CONCLUSIONS: Doppler tissue echocardiography and color M-mode Doppler flow could evaluate the serial deterioration in LV dysfunction throughout the pacing period. These were more useful in quantifying progressive LV dysfunction than conventional ehocardiographic techniques, and were probably relatively independent of preload. These techniques could be suitable for longitudinal evaluation in addition to the cross-sectional study.

Evaluation Studies↗

NASA NTRS1998

Effects of sleep loss, time of day, and extended mental work on implicit and explicit learning of sequences

Tacit knowledge is part of many professional skills and can be studied experimentally with implicit-learning paradigms. The authors explored the effects of 2 different stressors, loss of sleep and mental fatigue, on implicit learning in a serial-response time (RT) task. In the 1st experiment, 1 night of sleep deprivation was shown to impair implicit but not explicit sequence learning. In the 2nd experiment, no impairment of both types of sequence learning was found after 1.5 hr of mental work. Serial-RT performance, in contrast, suffered from both stressors. These findings suggest that sleep deprivation induces specific risks for automatic, skill-based behavior that are not present in consciously controlled performance.

Learning↗

NASA NTRS2000

Immunohistochemical myofiber typing and high-resolution myofibrillar lesion detection in LR white embedded muscle

We have developed a method of fixing, embedding, sectioning, and staining that allows high-resolution detection of myofibrillar structure and myosin immunocytochemical muscle fiber typing in serial semithin sections of LR White plastic embedded muscle at the light microscopic level. Traditional approaches, such as cryostat sections, permit fiber typing, but small myofibrillar lesions (1-3 sarcomeres) are difficult to detect because of section thickness. Semithin sections of hydrophobic resins do not stain well either histochemically or immunocytochemically. Electron microscopy can resolve lesions and discriminate fiber types based on morphology, but the sampling area is small. Our goal was to develop a rapid method for defining both fiber type and high-resolution primary myofibrillar lesion damage. Mild fixation (1-4% paraformaldehyde, 0. 05-0.1% glutaraldehyde) and embedment in a hydrophilic resin (LR White) were used. Myofibrillar structure was extremely well preserved at the light microscopic (LM) level, and lesions could be readily resolved in Toluidine blue stained 500-nm sections. Fiber type was defined by LM immunomyosin staining of serial plastic semithin sections, which demonstrated reciprocal staining patterns for "fast (Sigma M4276) and "total" (skeletal muscle) myosins (Sigma M7523). Copyright 2000 Wiley-Liss, Inc.

NASA Program Fundamental Space Biology↗

NASA NTRS2004

Prototype Motor Controllers Demonstrated for the James Webb Space Telescope Cryogenic Environment

NASA is in the process of designing the James Webb Space Telescope. This telescope will investigate images of objects in deep space (stars, galaxies, etc.) by using light in the infrared region of the light spectrum. To make such observations, the telescope must have light sensors that operate at very cold temperatures, near absolute zero. To achieve this low-temperature tolerance, designers must place the light sensors behind a Sun shield that will prevent sunlight, and its heat, from reaching the sensors. In this cold region inside the telescope, electric motors and some motor controls must operate at temperatures near 40 K (40 degrees above absolute zero). These motors will be used to position light filters needed by the telescope. There are motors that operate at the low temperatures, but there is little technology for low-temperature motor-control electronics. The drawing shows how the motors and their controls are positioned behind the Sun shield. Simplified version of the layout of the motor and control electronics that are located, as dictated by mission requirements, in the cold zone of the James Webb Space Telescope. A Sun shield provides protection and isolation of these electronics from the heat of the rays of the sun. Room temperature compoenets (control computer, motor select command, motor phase drive, power supply, parallel to serial, and sun shield) as well as 40-kelvin components (motor select, serial to parallel, and motors) are shown. The Low Temperature Electronics Group at the NASA Glenn Research Center has been working to develop motor control electronics that will operate at a temperature of 40 K. The group conducted tests to determine which electronic components will operate at such very low temperatures. Then, components that were determined to operate successfully at the low temperatures were used to design low-temperature motor-controller circuits. A prototype motor controller circuit was built, evaluated, and demonstrated to operate at 70 K. Next, Glenn researchers plan to determine circuit performance at much colder temperatures--down to 40 K. This low-temperature program was supported by the James Webb Space Telescope Electrical Systems Design Group at the NASA Goddard Space Flight Center and by the NASA Electronic Parts and Packaging Program at NASA Headquarters and the Jet Propulsion Laboratory.

Patterson, Richard L.↗